The Spectroscopy of Very Cold Gases

Unraveling the ultrafast dynamics of thermal-energy chemical reactions

In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.

Cavity Ring-Down Spectroscopy of Anthracene, 9-Methylanthracene, and 2-Methylanthracene in Supersonic Expansion

The S₀-S₁ absorption spectra of anthracene (C₁₄H₁₀), 9-methylanthracene (C₁₅H₁₂), and 2-methylanthracene (C₁₅H₁₂) are measured in the ultraviolet region between 330 and 375 nm (26,666 to 30,303 cm^-1) with cavity ring-down spectroscopy in supersonic free-jet expansions of argon. The associated vibronic band systems and their spectroscopic assignments are discussed and compared to previous studies performed using fluorescence excitation and dispersed fluorescence techniques. Density functional theory (DFT) calculations were carried out to study the structures and evaluate the vibrational transitions of the ground and excited states. Time-dependent DFT calculations of the first electronic excited states and Franck-Condon factor calculations were carried out to assist in the assignment of the experimentally measured vibronic bands. The vibronic spectra obtained in absorption agree well with fluorescence excitation spectra in terms of peak positions but exhibit different relative band intensities. We find a very good match between experimentally obtained vibronic line positions and the peak positions of the quantum chemically calculated Franck-Condon excitation lines.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Radical-Radical Reaction Dynamics Probed Using Millimeterwave Spectroscopy: Propargyl + NH2/ND2

We apply chirped-pulse uniform flow millimeterwave (CPUF-mmW) spectroscopy to study the complex multichannel reaction dynamics in the reaction between the propargyl and amino radicals (C₃H₃ + NH₂/ND₂), a radical-radical reaction of importance in the gas-phase chemistry of astrochemical environments and combustion systems. The photolytically generated radicals are allowed to react in a well-characterized quasi-uniform supersonic flow, and mmW rotational spectroscopy (70-93 GHz) is used for simultaneous detection of the reaction products: HCN, HNC, HC₃N, DCN, DNC, and DC₃N, while spectral intensities of the measured pure-rotational lines allow product branching to be quantified. High-level electronic structure calculations were used for theoretical prediction of the reaction pathways and branching. Experimentally deduced product branching fractions were compared with the results from statistical simulations based on the RRKM theory. Product branching was found to be strongly dependent on the excess internal energy of the C₃H₃ and NH₂/ND₂ reactants.

Proton Transfer in Nitromethane-Ammonia Clusters under VUV Single-Photon Ionization Explored by Infrared Spectroscopy and Theoretical Calculations

It is known that the acidity and reactivity of the CH bond can be enhanced after ionization. Also, this property plays a pivotal role in proton transfer reaction and in the formation of new molecules. Herein, infrared spectroscopy and high-precision quantum chemical calculations are used to study the neutral and cationic clusters of nitromethane-ammonia (CH₃NO₂-NH₃). It is found that in the neutral cluster, CH₃NO₂ and NH₃ are mainly bonded by three intermolecular hydrogen bonds, in which electrostatic contribution plays a major role. After vacuum ultraviolet (VUV) single-photon ionization of CH₃NO₂-NH₃, the positive charge redistributes from the ionized nitrogen atom of NH₃ to the CH₃NO₂ molecule immediately. Then, the proton of CH₃NO₂ transfers to NH₃ to form a proton-transferred type structure CH₂NO₂-NH₄⁺, without any effective energy barrier, due to the positive hyperconjugation of cationic nitromethane. A closed loop of positive charge transfer takes place in the CH₃NO₂-NH₃ cluster after VUV ionization. The present work demonstrates that both the proton transfer reaction and charge transfer process have occurred in the ionized CH₃NO₂-NH₃ cluster. Moreover, it is found that the proton transfer reaction is a result of the highly acidic CH bond caused by hyperconjugation between the σ (CH) bond and π orbital.

Long-lasting field-free alignment of large molecules inside helium nanodroplets

Molecules with their axes sharply confined in space, available through laser-induced alignment methods, are essential for many current experiments, including ultrafast molecular imaging. For these applications the aligning laser field should ideally be turned-off, to avoid undesired perturbations, and the strong alignment should last long enough that reactions and dynamics can be mapped out. Presently, this is only possible for small, linear molecules and for times less than 1 picosecond. Here, we demonstrate strong, field-free alignment of large molecules inside helium nanodroplets, lasting >10 picoseconds. One-dimensional or three-dimensional alignment is created by a slowly switched-on laser pulse, made field-free through rapid pulse truncation, and retained thanks to the impeding effect of the helium environment on molecular rotation. The opportunities field-free aligned molecules open are illustrated by measuring the alignment-dependent strong-field ionization yield of dibromothiophene oligomers. Our technique will enable molecular frame experiments, including ultrafast excited state dynamics, on a variety of large molecules and complexes.

Mid-infrared optical parametric oscillators and frequency combs for molecular spectroscopy

Review of mid-infrared optical parametric oscillators and frequency combs for high-resolution spectroscopy, including applications in trace gas detection and fundamental research.

Mass resolved IR spectroscopy of aniline–water aggregates

Aniline is the simplest aromatic amine and therefore it is a prototypical system to study the microhydration and excited state dynamics of aromatic amines.

Influence of dispersive forces on the final shape of a reverse micelle

Despite that they are comparatively weaker, C–H⋯π interactions have a strong influence on the final shape of molecular aggregates.

Complete Quantum State Selectivity in Cold Molecular Beams Using Deflection-Resistant Dark States in a STIRAP Configuration

One of the main goals of chemical dynamics is the creation of molecular beams composed of a single (vibrational, rotational, and magnetic) quantum state of choice. In this Letter, we propose a method to achieve complete quantum state selectivity by producing resistance to electromagnetically induced deflection (EID) and that the state to be selected can be "dialed in" at will. We illustrate the method by showing in detail how to purify thermal beams of the LiRb and IF molecules to yield molecular beams composed of a variety of prechosen single internal quantum states and/or superpositions of such states. We expect that this method will be implemented in all subsequent explorations of the fundamentals of chemical reactions and their control and the use of cold molecules as a vehicle for studying some of the most profound issues of quantum dynamics.

Resonance-enhanced multiphoton ionization mass spectrometry (REMPI-MS): applications for process analysis

Process analysis is an emerging discipline in analytical sciences that poses special requirements on analytical techniques, especially when conducted in an online manner. Mass spectrometric methods seem exceedingly suitable for this task, particularly if a soft ionization method is applied. Resonance-enhanced multiphoton ionization (REMPI) in combination with time-of-flight mass spectrometry (TOFMS) provides a selective and sensitive means for monitoring (poly)aromatic compounds in process flows. The properties of REMPI and various variations of the ionization process are presented. The potential of REMPI for process analysis is highlighted with several examples, and drawbacks of the method are also noted. Applications of REMPI-TOFMS for the detection and monitoring of aromatic species in a large variety of combustion processes comprising flames, vehicle exhaust, and incinerators are discussed. New trends in technical development and combination with other analytical methods are brought forward.

Prospect of Retrieving Vibrational Wave Function by Single-Object Scattering Sampling

The exact shape of wave functions has never been directly measured because an ensemble measurement is often overwhelmed by the contributions of highly populated configurations. In this work, we explore the possibility of directly obtaining vibrational wave functions by single-object scattering sampling (SOSS) using intense, ultrashort X-ray pulses provided by X-ray free electron lasers. Previously, single-molecule diffraction experiments using femtosecond X-ray pulses have been proposed with the prospect of determining three-dimensional structure of macromolecules without the need of single-crystal samples. In contrast to the previous proposals, SOSS is designed for obtaining the structural variations of constantly fluctuating molecules by sampling many single-shot, single-object scattering patterns. From the simulations on iodine molecules adopting various pulse characteristics and molecular parameters, we were able to reconstruct vibrational wave functions of molecular iodine and found that SOSS is feasible under appropriate experimental conditions.

Molecular beam mass spectrometry with tunable vacuum ultraviolet (VUV) synchrotron radiation

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics(1-4). Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water(1, 5-9). We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline(10) located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds(1). Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations(11, 12). By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species (1, 3).

Strength of NH···S Hydrogen Bonds in Methionine Residues Revealed by Gas-Phase IR/UV Spectroscopy

Despite of being ubiquitous in proteins, NHbackbone···S hydrogen bonds linking the sulfur atom of methionine or cysteine to backbone NH groups remain poorly documented. Here, we report vibrationally resolved IR NH stretch spectra of two methionine-containing dipeptides (Ac-Phe-Met-NH2 and Ac-Met-Phe-NH2). The conformations observed for both molecules, assigned with the help of DFT-D quantum chemistry, provide spectroscopic evidence for the formation of NHbackbone···S H-bonds, surprisingly strong enough to challenge the classical intrabackbone NH···O═C H-bonds. The methionine side chain is found to fold locally, forming a H-bond with the neighboring amide groups (NH(i) or NH(i+1)). Comparison with protein data bank structural information shows that such a local folding is also common in proteins where it concerns 24% of the methionine residues that have a sulfur atom linked to a backbone NH group. This convergence between the strength of these NH···S H-bonds and protein structural data illustrates their contribution to the stability of protein chains.

The spectroscopy of jet-cooled porphyrins: an insight into the vibronic structure of the Q band

We will present resonant two-photon ionization spectra for meso-tetraphenylporphyrin, H 2 TPP , measured under isolated conditions. The polycrystalline compound was vaporized, in vacuo, using both thermal and laser desorption, and seeded into a supersonic expansion of an inert-carrier gas. The molecules remain largely intact in the gaseous phase. However, the two techniques for vaporizing H 2 TPP give different internal temperatures for the isolated substrate, with greater vibrational cooling achieved using laser desorption. A comparison of the peak positions and intensities in the resonant two-photon ionization spectra of thermal- and laser-desorbed molecules provides an insight into the vibrational structure of the Q band. In particular, the greater contribution made by electronic transitions originating from higher vibrational levels in the ground state of H 2 TPP is emphasized. We conclude that vibronic coupling in the ground electronic state plays an important role in a quantum-mechanical interpretation of the Q band.

Desorption dynamics, internal energies, and imaging of organic molecules from surfaces with laser desorption and vacuum ultraviolet (VUV) photoionization

There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer by using laser-desorption VUV postionization shows 5 μm feature details while using a 30 μm laser spot size and 7 ns pulse duration. Applications of laser-desorption postionization to the analysis of cellulose, lignin, and humic acids are briefly discussed.

Multiple packets of neutral molecules revolving for over a mile

The level of control that one has over neutral molecules in beams dictates their possible applications. Here we experimentally demonstrate that state-selected, neutral molecules can be kept together in a few mm long packet for a distance of over one mile. This is accomplished in a circular arrangement of 40 straight electrostatic hexapoles through which the molecules propagate over 1000 times. Up to 19 packets of molecules have simultaneously been stored in this ring structure. This brings the realization of a molecular low-energy collider within reach.

The low-energy unimolecular reaction rate constants for the gas phase, Ni+-mediated dissociation of the C-C sigma bond in acetone

The time dependence of the gaseous unimolecular decomposition of the jet-cooled adduct ion, Ni+-OC(CH3)2, was monitored through selective detection of the Ni+CO fragment ion. Various resolved amounts of energy in the range 15600-18800 cm(-1) were supplied to initiate the dissociation reaction through absorption of laser photons by the title molecular complex. First-order rate constants, k(E), ranged from 113000 to 55000 s(-1) and decreased with decreasing amounts of internal excitation. The energy used to initiate the reaction is well below that required to fragment C-C sigma bonds and indicates the necessity of the Ni+ cation to induce bond activation and fragmentation. These measurements are carried out in a unique apparatus and represent the first direct kinetic study of such catalytic type reactions.

Conformations of alpha-aminobutyric acid in the gas phase

A laser-ablation molecular-beam Fourier transform microwave (LA-MB-FTMW) spectrometer has been successfully applied to the structural study of alpha-aminobutyric acid. Three neutral conformers have been identified in the gas phase by comparing their experimental rotational and 14N nuclear quadrupole coupling parameters with those predicted by ab initio calculations at the MP2/6-311++G(d,p) level. The most stable conformer is stabilized by a bifurcated amine-to-carbonyl hydrogen bond (N--HO=C) and a cis-COOH group, and the side-chain adopts a configuration with a torsion angle tau(C(gamma)-C(beta)-C(alpha)-C') of about 180 degrees. The second most stable conformer exhibits the same configuration for the amino acid skeleton but adopts a different orientation for the side chain with tau(C(gamma)-C(beta)-C(alpha)-C') approximately -60 degrees. In the third conformer an intramolecular hydrogen bond is established between the hydroxyl group and the nitrogen atom (NH--O), with a side-chain orientation similar to that of the most stable conformer.

Conformational study of 2-phenylethylamine by molecular-beam Fourier transform microwave spectroscopy

The conformational preferences of the simplest amine neurotransmitter 2-phenylethylamine have been investigated using molecular beam Fourier transform microwave (MB-FTMW) spectroscopy. Two new conformers have been observed together with the two previously reported by Godfrey et al. [J. Am. Chem. Soc., 1995, 117, 8204]. The (14)N nuclear quadrupole hyperfine structure has been resolved for all four conformers. Comparison of the experimental rotational and quadrupole coupling constants with those calculated theoretically provides a conclusive test for the identification of all conformers. The two most stable conformers present a gauche (folded) disposition of the alkyl-amine chain and are stabilised by a weak NH...pi interaction between the amino group and the aromatic ring. The other two conformers show an anti (extended) arrangement of the alkyl-amine chain. Tunnelling splittings have been observed in the spectrum of one of the anti conformers. The post expansion relative abundances in the supersonic jet have been also investigated and related to the conformer energies.

Probing thymine with laser ablation molecular beam Fourier transform microwave spectroscopy

Laser ablation in combination with molecular beam Fourier transform microwave spectroscopy has been used to establish unambiguously the presence of the diketo form of thymine in the gas phase and to obtain its structure.

The Shape of Leucine in the Gas Phase

Two structures of neutral leucine are detected in the jet-cooled rotational spectrum of a laser-ablation molecular-beam Fourier transform microwave (LA-MB-FTMW) experiment. The comparison between the experimental rotational and (14)N nuclear quadrupole coupling constants and those calculated ab initio provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by a N-H...O=C intramolecular hydrogen bond and a cis-COOH interaction, while a higher-energy conformer exhibits a N...H-O intramolecular hydrogen bond and trans-COOH, as in lower aliphatic amino acids. The isobutyl side chain adopts the same configuration in the two conformers of leucine, characterized by a trans arrangement of the C'-C(alpha)-C(beta)-C(gamma)-C(delta) chain. The differences with the preferred side chain configurations observed in valine and isoleucine are discussed.

Quantum Simulation of a Hydrated Noradrenaline Analog with the Torsional Path Integral Method

An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.

Gas-Phase Structure ofN,N-Dimethylglycine

Three conformers of the neutral amino acid N,N-dimethylglycine [(CH3)2NCH2COOH] were detected in a supersonic expansion by a combination of laser ablation (LA) and molecular-beam Fourier transform microwave (MB-FTMW) spectroscopy. A bifurcated methyl-to-carbonyl (C--HO==C) weak intramolecular hydrogen bond might stabilise the most stable conformer of C(s) symmetry. The second most stable conformer of C1 symmetry has a hydrogen bond between the hydroxyl group and the lone pair at the nitrogen atom (NH--O). The r(s) and r0 structures were derived for this conformer from the rotational data for the parent and six minor 13C, 15N and OD isotopomers. A third conformer exhibits a cis-carboxyl functional group and C1 symmetry. Ab initio MP2/6-311++G(d,p) predictions of the spectroscopic parameters were useful in analysing the spectra. In particular, the agreement of the nuclear quadrupole coupling constants with those calculated was conclusive in identifying the different conformers.

Mass-selected resonance-enhanced multiphoton ionisation spectra of laser-desorbed molecules for environmental analysis: 16 representative polycyclic aromatic compounds

Mass-selected gas-phase UV spectra of laser-desorbed molecules at room temperature have been measured via resonance-enhanced multiphoton ionisation (REMPI) and time-of-flight mass selection. The wavelength range of 260 to 320 nm is optimal for detection of polycyclic aromatic hydrocarbons (PAHs) using REMPI-mass spectrometry. A new laser desorption/laser ionisation source has been used which features a compact size and thermal equilibrium of the desorbed molecules. 16 PAHs have been investigated which have been selected by the US Environmental Protection Agency (EPA). These 16 EPA-PAHs are commonly used world-wide to characterise the PAH-load of environmental samples.

Threshold photoionization in time-of-flight mass spectrometry

Multi-photon excitation in a time-of-flight mass spectrometer (TOF-MS) is shown to lead to threshold ions with defined internal energy. A powerful technique for the production of threshold ions is based on the excitation of high long-lived Rydberg states embedded in the ionization continuum. The Rydberg molecules are separated with suitable separation techniques from ions produced by a direct multi-photon ionization process. Finally, the ionization of the Rydberg molecules in a delayed pulsed electric field leads to threshold ions. This work reviews several separation techniques, and reports on applications of threshold ionization for investigation of the structure, energetics, and dynamics of neutral molecules, molecular cations, and cluster cations.

Time-of-flight mass spectrometry: State-of the-art in chemical analysis and molecular science

Time-of-flight instruments form a well-established group of mass spectrometers, with its popularity still increasing. This article gives a survey of the technical basics and important instrumental developments in this field. Special notice is taken of factors that limit the mass resolution and to techniques to overcome them. The possibilities to perform tandem MS experiments in flight-time mass analyzers and their combination with ion-trapping devices are discussed. Finally, some examples of the modern applications of these instruments in molecular science and instrumental analysis are reviewed. © 1997 John Wiley & Sons, Inc.